Hi,
until recently I was using Bowtie2 with no problems. Today I am trying to build a new index e.g.
bowtie2-build test.fna test
the fasta file was some plasmid sequence but kept giving me the below error after a few mintues 'stalled':
**********************************************
fchr[A]: 0
fchr[C]: 51813
fchr[G]: 65001
fchr[T]: 84678
fchr[$]: 126810
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4236774 bytes to primary EBWT file: p.1.bt2
Wrote 31708 bytes to secondary EBWT file: p.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 126810
bwtLen: 126811
sz: 31703
bwtSz: 31703
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 7926
offsSz: 31704
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 661
numLines: 661
ebwtTotLen: 42304
ebwtTotSz: 42304
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:00
Warning: Empty fasta file: 'test.fna'
Warning: All fasta inputs were empty
Total time for backward call to driver() for mirror index: 00:00:41
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 test.fna p
Deleting "p.3.bt2" file written during aborted indexing attempt.
Deleting "p.4.bt2" file written during aborted indexing attempt.
Deleting "p.1.bt2" file written during aborted indexing attempt.
Deleting "p.2.bt2" file written during aborted indexing attempt.
******************************************************
I experimented with the file size, and irrespective of the actual sequence used
my limit is 126811 bases.
Any longer and the program gives the 'empty fasta file' error. Anyone have any clue what is going on?? previously I have had no problems iwth much bigger files on the same machine (80GB RAM).
Thanks,
S
until recently I was using Bowtie2 with no problems. Today I am trying to build a new index e.g.
bowtie2-build test.fna test
the fasta file was some plasmid sequence but kept giving me the below error after a few mintues 'stalled':
**********************************************
fchr[A]: 0
fchr[C]: 51813
fchr[G]: 65001
fchr[T]: 84678
fchr[$]: 126810
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4236774 bytes to primary EBWT file: p.1.bt2
Wrote 31708 bytes to secondary EBWT file: p.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 126810
bwtLen: 126811
sz: 31703
bwtSz: 31703
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 7926
offsSz: 31704
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 661
numLines: 661
ebwtTotLen: 42304
ebwtTotSz: 42304
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:00
Warning: Empty fasta file: 'test.fna'
Warning: All fasta inputs were empty
Total time for backward call to driver() for mirror index: 00:00:41
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 test.fna p
Deleting "p.3.bt2" file written during aborted indexing attempt.
Deleting "p.4.bt2" file written during aborted indexing attempt.
Deleting "p.1.bt2" file written during aborted indexing attempt.
Deleting "p.2.bt2" file written during aborted indexing attempt.
******************************************************
I experimented with the file size, and irrespective of the actual sequence used
my limit is 126811 bases.
Any longer and the program gives the 'empty fasta file' error. Anyone have any clue what is going on?? previously I have had no problems iwth much bigger files on the same machine (80GB RAM).
Thanks,
S
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